7VJU

Crystal Structure of terephthalate dioxygenase from Comamonas testosteroni KF1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.160 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Insights into Dihydroxylation of Terephthalate, a Product of Polyethylene Terephthalate Degradation.

Mahto, J.K.Neetu, N.Sharma, M.Dubey, M.Vellanki, B.P.Kumar, P.

(2022) J Bacteriol 204: e0054321-e0054321

  • DOI: https://doi.org/10.1128/JB.00543-21
  • Primary Citation of Related Structures:  
    7VJU

  • PubMed Abstract: 

    Biodegradation of terephthalate (TPA) is a highly desired catabolic process for the bacterial utilization of this polyethylene terephthalate (PET) depolymerization product, but to date, the structure of terephthalate dioxygenase (TPDO), a Rieske oxygenase (RO) that catalyzes the dihydroxylation of TPA to a cis -diol, is unavailable. In this study, we characterized the steady-state kinetics and first crystal structure of TPDO from Comamonas testosteroni KF1 (TPDO KF1 ). TPDO KF1 exhibited substrate specificity for TPA ( k cat / K m = 57 ± 9 mM -1  s -1 ). The TPDO KF1 structure harbors characteristic RO features as well as a unique catalytic domain that rationalizes the enzyme's function. The docking and mutagenesis studies reveal that its substrate specificity for TPA is mediated by the Arg309 and Arg390 residues, positioned on opposite faces of the active site. Additionally, residue Gln300 is also proven to be crucial for the activity, as its mutation to alanine decreases the activity ( k cat ) by 80%. This study delineates the structural features that dictate the substrate recognition and specificity of TPDO. IMPORTANCE Global plastic pollution has become the most pressing environmental issue. Recent studies on enzymes depolymerizing polyethylene terephthalate plastic into terephthalate (TPA) show some potential for tackling this. Microbial utilization of this released product, TPA, is an emerging and promising strategy for waste-to-value creation. Research in the last decade has identified terephthalate dioxygenase (TPDO) as being responsible for initiating the enzymatic degradation of TPA in a few Gram-negative and Gram-positive bacteria. Here, we determined the crystal structure of TPDO from Comamonas testosteroni KF1 and revealed that it possesses a unique catalytic domain featuring two basic residues in the active site to recognize TPA. Biochemical and mutagenesis studies demonstrated the crucial residues responsible for the substrate specificity of this enzyme.


  • Organizational Affiliation

    Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, Uttarakhand, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rieske (2Fe-2S) domain protein
A, C, E
413Comamonas testosteroni KF-1Mutation(s): 0 
Gene Names: CtesDRAFT_PD2130
UniProt
Find proteins for B7WRJ9 (Comamonas testosteroni (strain DSM 14576 / KF-1))
Explore B7WRJ9 
Go to UniProtKB:  B7WRJ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7WRJ9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Aromatic-ring-hydroxylating dioxygenase beta subunit
B, D, F
154Comamonas testosteroni KF-1Mutation(s): 0 
Gene Names: CtesDRAFT_PD2129
UniProt
Find proteins for B7WRJ8 (Comamonas testosteroni (strain DSM 14576 / KF-1))
Explore B7WRJ8 
Go to UniProtKB:  B7WRJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7WRJ8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
M [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
G [auth A],
P [auth C],
Y [auth E]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
FA [auth F]
I [auth A]
J [auth A]
AA [auth E],
BA [auth E],
FA [auth F],
I [auth A],
J [auth A],
O [auth C],
R [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
DA [auth E]
EA [auth E]
GA [auth F]
L [auth A]
N [auth B]
DA [auth E],
EA [auth E],
GA [auth F],
L [auth A],
N [auth B],
S [auth C],
T [auth C],
U [auth C],
W [auth D],
X [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth E],
K [auth A],
V [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
H [auth A],
Q [auth C],
Z [auth E]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.561α = 90
b = 134.213β = 90
c = 145.01γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/HRD/NBA/37/01/2015 (VIII)

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description